proteobench.io.params.proline module

Proline Studio is a quantification tool. The search engine is often Mascot. The parameters are provided per raw file in separate sheets of an Excel file.

Relevant information in sheets: - “Search settings and infos”, - “Import and filters” - “Quant config”

proteobench.io.params.proline.extract_params(fname: str, json_file='/home/docs/checkouts/readthedocs.org/user_builds/proteobench/envs/v0.15.0/lib/python3.11/site-packages/proteobench/io/params/json/Quant/quant_lfq_DDA_ion.json') → ProteoBenchParameters

Parse Proline Studio parameter file (Excel) and extract relevant parameters.

Parameters:

fname (str) – The path to the Proline Studio Excel parameter file.

Returns:

The extracted parameters encapsulated in a ProteoBenchParameters object.

Return type:

ProteoBenchParameters

proteobench.io.params.proline.find_charge(string: str) → List[int]

Extract charge states from a string using a regular expression.

Parameters:

string (str) – The string containing charge states.

Returns:

A list of charge states as integers.

Return type:

List[int]

proteobench.io.params.proline.find_min_pep_length(string: str) → int

Extract the minimum peptide length from a string using a regular expression.

Parameters:

string (str) – The string containing the minimum peptide length.

Returns:

The minimum peptide length as an integer.

Return type:

int